> top > docs > PMC:7443692 > spans > 63432-68244 > annotations

PMC:7443692 / 63432-68244 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-sample-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T432 131-138 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T433 217-224 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T434 471-478 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T435 977-984 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T436 1311-1318 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T437 1702-1709 Chemical denotes glycans http://purl.obolibrary.org/obo/CHEBI_18154
T438 2183-2190 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T439 2240-2247 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T440 2253-2265 Chemical denotes glycoprotein http://purl.obolibrary.org/obo/CHEBI_17089
T441 2379-2389 Chemical denotes asparagine http://purl.obolibrary.org/obo/CHEBI_22653
T442 2539-2546 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T443 2741-2746 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T444 2840-2845 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T445 3372-3384 Chemical denotes carbohydrate http://purl.obolibrary.org/obo/CHEBI_16646
T446 3389-3396 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T447 3803-3811 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T448 4020-4025 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T449 4087-4092 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T450 4100-4107 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sample-PD-NCBITaxon

Id Subject Object Predicate Lexical cue ncbi_taxonomy_id
T173 73-83 Species denotes SARS-CoV-2 NCBItxid:2697049
T174 90-95 Species denotes Human NCBItxid:9606
T175 110-120 Species denotes SARS-CoV-2 NCBItxid:2697049
T176 2170-2180 Species denotes SARS-CoV-2 NCBItxid:2697049

LitCovid-sample-sentences

Id Subject Object Predicate Lexical cue
T428 0-109 Sentence denotes 3D Structural Modeling and Molecular Dynamics Simulation of Glycosylated SARS-CoV-2 S and Human ACE2 Proteins
T429 110-412 Sentence denotes SARS-CoV-2 Spike (S) protein structure and ACE2 co-complex – A 3D structure of the prefusion form of the S protein (RefSeq: YP_009724390.1, UniProt: P0DTC2 SPIKE_SARS2), based on a Cryo-EM structure (PDB code 6VSB) (Wrapp et al., 2020), was obtained from the SWISS-MODEL server (swissmodel.expasy.org).
T430 413-479 Sentence denotes The model has 95% coverage (residues 27 to 1146) of the S protein.
T431 480-641 Sentence denotes The receptor binding domain (RBD) in the “open” conformation was replaced with the RBD from an ACE2 co-complex (PDB code 6M0J) by grafting residues C336 to V524.
T432 642-910 Sentence denotes Glycoform generation – Glycans (detected by glycomics) were selected for installation on glycosylated S and ACE2 sequons (detected by glycoproteomics) based on three sets of criteria designed to reasonably capture different aspects of glycosylation microheterogeneity.
T433 911-1250 Sentence denotes We denote the first of these glycoform models as “Abundance.” The glycans selected for installation to generate the Abundance model were chosen because they were identified as the most abundant glycan structure (detected by glycomics) that matched the most abundant glycan composition (detected by glycoproteomics) at each individual site.
T434 1251-1636 Sentence denotes We denote the second glycoform model as “Oxford Class.” The glycans selected for installation to generate the Oxford Class model were chosen because they were the most abundant glycan structure, (detected by glycomics) that was contained within the most highly represented Oxford classification group (detected by glycoproteomics) at each individual site (Figure S7; Tables S1 and S8).
T435 1637-2071 Sentence denotes Finally, we denote the third glycoform model as “Processed.” The glycans selected for installation to generate the Processed model were chosen because they were the most highly trimmed, elaborated, or terminally decorated structure (detected by glycomics) that corresponded to a composition (detected by glycoproteomics) which was present at ≥ 1/3rd of the abundance of the most highly represented composition at each site (Table S1).
T436 2072-2248 Sentence denotes 3D structures of the three glycoforms (Abundance, Oxford Class, Processed) were generated for the SARS-CoV-2 S protein alone, and in complex with the glycosylated ACE2 protein.
T437 2249-2612 Sentence denotes The glycoprotein builder available at GLYCAM-Web (www.glycam.org) was employed together with an in-house program that adjusts the asparagine side chain torsion angles and glycosidic linkages within known low-energy ranges (Nivedha et al., 2014) to relieve any atomic overlaps with the core protein, as described previously (Grant et al., 2016; Peng et al., 2017).
T438 2613-2812 Sentence denotes Energy minimization and Molecular dynamics (MD) simulations – Each glycosylated structure was placed in a periodic box of TIP3P water molecules with a 10 Å buffer between the solute and the box edge.
T439 2813-3008 Sentence denotes Energy minimization of all atoms was performed for 20,000 steps (10,000 steepest decent, followed by 10,000 conjugant gradient) under constant pressure (1 atm) and temperature (300 K) conditions.
T440 3009-3251 Sentence denotes All MD simulations were performed under nPT conditions with the CUDA implementation of the PMEMD (Götz et al., 2012; Salomon-Ferrer et al., 2013) simulation code, as present in the Amber14 software suite (University of California, San Diego).
T441 3252-3420 Sentence denotes The GLYCAM06j force field (Kirschner et al., 2008) and Amber14SB force field (Maier et al., 2015) were employed for the carbohydrate and protein moieties, respectively.
T442 3421-3614 Sentence denotes A Berendsen barostat with a time constant of 1 ps was employed for pressure regulation, while a Langevin thermostat with a collision frequency of 2 ps-1 was employed for temperature regulation.
T443 3615-3667 Sentence denotes A nonbonded interaction cut-off of 8 Å was employed.
T444 3668-3777 Sentence denotes Long-range electrostatics were treated with the particle-mesh Ewald (PME) method (Darden and Pedersen, 1993).
T445 3778-3912 Sentence denotes Covalent bonds involving hydrogen were constrained with the SHAKE algorithm, allowing an integration time step of 2 fs to be employed.
T446 3913-4026 Sentence denotes The energy minimized coordinates were equilibrated at 300K over 400 ps with restraints on the solute heavy atoms.
T447 4027-4275 Sentence denotes Each system was then equilibrated with restraints on the Ca atoms of the protein for 1ns, prior to initiating 4 independent 250 ns production MD simulations with random starting seeds for a total time of 1 μs per system, with no restraints applied.
T448 4276-4303 Sentence denotes Antigenic surface analysis.
T449 4304-4658 Sentence denotes A series of 3D structure snapshots of the simulation were taken at 1 ns intervals and analyzed in terms of their ability to interact with a spherical probe based on the average size of hypervariable loops present in an antibody complementarity determining region (CDR), as described recently (https://www.biorxiv.org/content/10.1101/2020.04.07.030445v2).
T450 4659-4812 Sentence denotes The percentage of simulation time each residue was exposed to the AbASA probe was calculated and plotted onto both the 3D structure and primary sequence.

LitCovid-sample-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T105 73-83 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T106 110-120 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T107 2170-2180 Disease denotes SARS-CoV-2 http://purl.obolibrary.org/obo/MONDO_0100096
T108 3737-3740 Disease denotes PME http://purl.obolibrary.org/obo/MONDO_0020074

LitCovid-sample-UniProt

Id Subject Object Predicate Lexical cue uniprot_id
T5229 96-100 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5230 127-138 Protein denotes (S) protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5263 153-157 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5264 171-175 Protein denotes A 3D https://www.uniprot.org/uniprot/Q96AK3|https://www.uniprot.org/uniprot/Q7Z2N6|https://www.uniprot.org/uniprot/Q7Z2N5|https://www.uniprot.org/uniprot/Q7Z2N2|https://www.uniprot.org/uniprot/Q5JZ91
T5269 215-224 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5302 469-478 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5335 509-512 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5344 563-566 Protein denotes RBD https://www.uniprot.org/uniprot/Q63492|https://www.uniprot.org/uniprot/Q63491|https://www.uniprot.org/uniprot/Q62815|https://www.uniprot.org/uniprot/Q62691|https://www.uniprot.org/uniprot/Q01542|https://www.uniprot.org/uniprot/P27732|https://www.uniprot.org/uniprot/O09024|https://www.uniprot.org/uniprot/O09023|https://www.uniprot.org/uniprot/O09022
T5353 575-579 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5354 750-754 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5355 2181-2190 Protein denotes S protein https://www.uniprot.org/uniprot/Q9UIP0|https://www.uniprot.org/uniprot/Q9UIN9|https://www.uniprot.org/uniprot/Q9UIN8|https://www.uniprot.org/uniprot/Q9UIN7|https://www.uniprot.org/uniprot/Q9UIN6|https://www.uniprot.org/uniprot/Q9UBH8|https://www.uniprot.org/uniprot/Q9NRH8|https://www.uniprot.org/uniprot/Q9NRH7|https://www.uniprot.org/uniprot/Q9NRH6|https://www.uniprot.org/uniprot/Q9NRH5|https://www.uniprot.org/uniprot/Q9NRH4|https://www.uniprot.org/uniprot/Q9NPG5|https://www.uniprot.org/uniprot/Q9NPE0|https://www.uniprot.org/uniprot/Q9NP52|https://www.uniprot.org/uniprot/Q95IF9|https://www.uniprot.org/uniprot/Q8N5P3|https://www.uniprot.org/uniprot/Q8IZU6|https://www.uniprot.org/uniprot/Q8IZU5|https://www.uniprot.org/uniprot/Q8IZU4|https://www.uniprot.org/uniprot/Q86Z04|https://www.uniprot.org/uniprot/Q7YR44|https://www.uniprot.org/uniprot/Q7LA71|https://www.uniprot.org/uniprot/Q7LA70|https://www.uniprot.org/uniprot/Q5STD2|https://www.uniprot.org/uniprot/Q5SQ85|https://www.uniprot.org/uniprot/Q1XI16|https://www.uniprot.org/uniprot/Q1XI12|https://www.uniprot.org/uniprot/Q15517|https://www.uniprot.org/uniprot/O43509|https://www.uniprot.org/uniprot/O19084|https://www.uniprot.org/uniprot/B0UYZ7|https://www.uniprot.org/uniprot/B0S7V2|https://www.uniprot.org/uniprot/A5A6L9
T5388 2235-2239 Protein denotes ACE2 https://www.uniprot.org/uniprot/Q9UFZ6
T5389 2253-2265 Protein denotes glycoprotein https://www.uniprot.org/uniprot/Q9QSP1|https://www.uniprot.org/uniprot/Q9QJT6|https://www.uniprot.org/uniprot/Q9JGT4|https://www.uniprot.org/uniprot/Q9IPJ6|https://www.uniprot.org/uniprot/Q9DIC6|https://www.uniprot.org/uniprot/Q91DS0|https://www.uniprot.org/uniprot/Q91C28|https://www.uniprot.org/uniprot/Q8QQA2|https://www.uniprot.org/uniprot/Q8QPE5|https://www.uniprot.org/uniprot/Q8QPE4|https://www.uniprot.org/uniprot/Q8QPE3|https://www.uniprot.org/uniprot/Q8JTH0|https://www.uniprot.org/uniprot/Q8BDV6|https://www.uniprot.org/uniprot/Q8B6J6|https://www.uniprot.org/uniprot/Q8B0I1|https://www.uniprot.org/uniprot/Q8B0H6|https://www.uniprot.org/uniprot/Q8B0H1|https://www.uniprot.org/uniprot/Q89669|https://www.uniprot.org/uniprot/Q85213|https://www.uniprot.org/uniprot/Q82706|https://www.uniprot.org/uniprot/Q82683|https://www.uniprot.org/uniprot/Q82020|https://www.uniprot.org/uniprot/Q787B5|https://www.uniprot.org/uniprot/Q77SK0|https://www.uniprot.org/uniprot/Q77N36|https://www.uniprot.org/uniprot/Q76G52|https://www.uniprot.org/uniprot/Q75T09|https://www.uniprot.org/uniprot/Q6X1D5|https://www.uniprot.org/uniprot/Q6X1D1|https://www.uniprot.org/uniprot/Q6TYA0|https://www.uniprot.org/uniprot/Q6E0W7|https://www.uniprot.org/uniprot/Q66T62|https://www.uniprot.org/uniprot/Q5VKP3|https://www.uniprot.org/uniprot/Q5VKN9|https://www.uniprot.org/uniprot/Q5K2K4|https://www.uniprot.org/uniprot/Q5IX93|https://www.uniprot.org/uniprot/Q5IX92|https://www.uniprot.org/uniprot/Q5IX91|https://www.uniprot.org/uniprot/Q5IX90|https://www.uniprot.org/uniprot/Q5IX89|https://www.uniprot.org/uniprot/Q5IX88|https://www.uniprot.org/uniprot/Q5IX87|https://www.uniprot.org/uniprot/Q5GA86|https://www.uniprot.org/uniprot/Q58FH1|https://www.uniprot.org/uniprot/Q4VKV3|https://www.uniprot.org/uniprot/Q4F900|https://www.uniprot.org/uniprot/Q49LL3|https://www.uniprot.org/uniprot/Q49IU2|https://www.uniprot.org/uniprot/Q49IU1|https://www.uniprot.org/uniprot/Q49IT9|https://www.uniprot.org/uniprot/Q49IT8|https://www.uniprot.org/uniprot/Q49AV0|https://www.uniprot.org/uniprot/Q0GBY1|https://www.uniprot.org/uniprot/Q0GBX6|https://www.uniprot.org/uniprot/Q08089|https://www.uniprot.org/uniprot/P32595|https://www.uniprot.org/uniprot/P32550|https://www.uniprot.org/uniprot/P19462|https://www.uniprot.org/uniprot/P16288|https://www.uniprot.org/uniprot/P15199|https://www.uniprot.org/uniprot/P13180|https://www.uniprot.org/uniprot/P0C572|https://www.uniprot.org/uniprot/P08667|https://www.uniprot.org/uniprot/P08163|https://www.uniprot.org/uniprot/P07923|https://www.uniprot.org/uniprot/P04884|https://www.uniprot.org/uniprot/P04883|https://www.uniprot.org/uniprot/P04882|https://www.uniprot.org/uniprot/P03524|https://www.uniprot.org/uniprot/P03522|https://www.uniprot.org/uniprot/O92284|https://www.uniprot.org/uniprot/O56677|https://www.uniprot.org/uniprot/O10236|https://www.uniprot.org/uniprot/J7HBH4|https://www.uniprot.org/uniprot/D8V075|https://www.uniprot.org/uniprot/A7WNB3|https://www.uniprot.org/uniprot/A4UHQ6|https://www.uniprot.org/uniprot/A4UHQ1|https://www.uniprot.org/uniprot/A3RM22|https://www.uniprot.org/uniprot/A3F5R8|https://www.uniprot.org/uniprot/A3F5R3|https://www.uniprot.org/uniprot/A3F5Q8|https://www.uniprot.org/uniprot/A3F5N3|https://www.uniprot.org/uniprot/A3F5M3|https://www.uniprot.org/uniprot/A3F5L8
T5474 2534-2546 Protein denotes core protein https://www.uniprot.org/uniprot/Q9QBF2|https://www.uniprot.org/uniprot/Q9QAB9|https://www.uniprot.org/uniprot/Q9Q9F7|https://www.uniprot.org/uniprot/Q9Q6P4|https://www.uniprot.org/uniprot/Q9E6S6|https://www.uniprot.org/uniprot/Q9DKQ7|https://www.uniprot.org/uniprot/Q9DKQ6|https://www.uniprot.org/uniprot/Q9DKQ5|https://www.uniprot.org/uniprot/Q99D35|https://www.uniprot.org/uniprot/Q99BK4|https://www.uniprot.org/uniprot/Q999T0|https://www.uniprot.org/uniprot/Q98803|https://www.uniprot.org/uniprot/Q91B85|https://www.uniprot.org/uniprot/Q8JKE4|https://www.uniprot.org/uniprot/Q8B648|https://www.uniprot.org/uniprot/Q89579|https://www.uniprot.org/uniprot/Q89278|https://www.uniprot.org/uniprot/Q89277|https://www.uniprot.org/uniprot/Q89276|https://www.uniprot.org/uniprot/Q89275|https://www.uniprot.org/uniprot/Q88879|https://www.uniprot.org/uniprot/Q88878|https://www.uniprot.org/uniprot/Q88877|https://www.uniprot.org/uniprot/Q88788|https://www.uniprot.org/uniprot/Q88787|https://www.uniprot.org/uniprot/Q88786|https://www.uniprot.org/uniprot/Q88785|https://www.uniprot.org/uniprot/Q88784|https://www.uniprot.org/uniprot/Q88783|https://www.uniprot.org/uniprot/Q88782|https://www.uniprot.org/uniprot/Q88781|https://www.uniprot.org/uniprot/Q88671|https://www.uniprot.org/uniprot/Q88670|https://www.uniprot.org/uniprot/Q88669|https://www.uniprot.org/uniprot/Q88668|https://www.uniprot.org/uniprot/Q88667|https://www.uniprot.org/uniprot/Q88666|https://www.uniprot.org/uniprot/Q88665|https://www.uniprot.org/uniprot/Q88664|https://www.uniprot.org/uniprot/Q88663|https://www.uniprot.org/uniprot/Q88662|https://www.uniprot.org/uniprot/Q88661|https://www.uniprot.org/uniprot/Q88655|https://www.uniprot.org/uniprot/Q88654|https://www.uniprot.org/uniprot/Q88653|https://www.uniprot.org/uniprot/Q88652|https://www.uniprot.org/uniprot/Q88651|https://www.uniprot.org/uniprot/Q88650|https://www.uniprot.org/uniprot/Q88649|https://www.uniprot.org/uniprot/Q88648|https://www.uniprot.org/uniprot/Q88647|https://www.uniprot.org/uniprot/Q88646|https://www.uniprot.org/uniprot/Q88645|https://www.uniprot.org/uniprot/Q88644|https://www.uniprot.org/uniprot/Q88643|https://www.uniprot.org/uniprot/Q88642|https://www.uniprot.org/uniprot/Q88493|https://www.uniprot.org/uniprot/Q88479|https://www.uniprot.org/uniprot/Q88478|https://www.uniprot.org/uniprot/Q88477|https://www.uniprot.org/uniprot/Q88476|https://www.uniprot.org/uniprot/Q88475|https://www.uniprot.org/uniprot/Q82983|https://www.uniprot.org/uniprot/Q82928|https://www.uniprot.org/uniprot/Q82927|https://www.uniprot.org/uniprot/Q82926|https://www.uniprot.org/uniprot/Q82925|https://www.uniprot.org/uniprot/Q82924|https://www.uniprot.org/uniprot/Q82923|https://www.uniprot.org/uniprot/Q82922|https://www.uniprot.org/uniprot/Q82921|https://www.uniprot.org/uniprot/Q82920|https://www.uniprot.org/uniprot/Q81164|https://www.uniprot.org/uniprot/Q81102|https://www.uniprot.org/uniprot/Q7T6D2|https://www.uniprot.org/uniprot/Q7T4P5|https://www.uniprot.org/uniprot/Q7T4P4|https://www.uniprot.org/uniprot/Q76R61|https://www.uniprot.org/uniprot/Q6YMS4|https://www.uniprot.org/uniprot/Q6YMS3|https://www.uniprot.org/uniprot/Q6QLS0|https://www.uniprot.org/uniprot/Q6QLR9|https://www.uniprot.org/uniprot/Q6QLR8|https://www.uniprot.org/uniprot/Q6QLR7|https://www.uniprot.org/uniprot/Q6QLR6|https://www.uniprot.org/uniprot/Q6QLR5|https://www.uniprot.org/uniprot/Q6PX46|https://www.uniprot.org/uniprot/Q6J3P1|https://www.uniprot.org/uniprot/Q6DV88|https://www.uniprot.org/uniprot/Q6DLV0|https://www.uniprot.org/uniprot/Q69608|https://www.uniprot.org/uniprot/Q69422|https://www.uniprot.org/uniprot/Q67924|https://www.uniprot.org/uniprot/Q67868|https://www.uniprot.org/uniprot/Q66450|https://www.uniprot.org/uniprot/Q66406|https://www.uniprot.org/uniprot/Q66356|https://www.uniprot.org/uniprot/Q66355|https://www.uniprot.org/uniprot/Q66354|https://www.uniprot.org/uniprot/Q66353|https://www.uniprot.org/uniprot/Q66352|https://www.uniprot.org/uniprot/Q66351|https://www.uniprot.org/uniprot/Q66350|https://www.uniprot.org/uniprot/Q66349|https://www.uniprot.org/uniprot/Q66348|https://www.uniprot.org/uniprot/Q66347|https://www.uniprot.org/uniprot/Q64897|https://www.uniprot.org/uniprot/Q5WPU5|https://www.uniprot.org/uniprot/Q5UCB8|https://www.uniprot.org/uniprot/Q5UB51|https://www.uniprot.org/uniprot/Q58HT7|https://www.uniprot.org/uniprot/Q45RQ2|https://www.uniprot.org/uniprot/Q32ZE1|https://www.uniprot.org/uniprot/Q32ZE0|https://www.uniprot.org/uniprot/Q32ZD7|https://www.uniprot.org/uniprot/Q32ZD5|https://www.uniprot.org/uniprot/Q32ZD4|https://www.uniprot.org/uniprot/Q2YHF2|https://www.uniprot.org/uniprot/Q2YHF0|https://www.uniprot.org/uniprot/Q20II6|https://www.uniprot.org/uniprot/Q1X881|https://www.uniprot.org/uniprot/Q1X880|https://www.uniprot.org/uniprot/Q14F58|https://www.uniprot.org/uniprot/Q102J3|https://www.uniprot.org/uniprot/Q074N0|https://www.uniprot.org/uniprot/Q04538|https://www.uniprot.org/uniprot/Q01299|https://www.uniprot.org/uniprot/P89314|https://www.uniprot.org/uniprot/P89313|https://www.uniprot.org/uniprot/P69712|https://www.uniprot.org/uniprot/P69711|https://www.uniprot.org/uniprot/P69710|https://www.uniprot.org/uniprot/P69709|https://www.uniprot.org/uniprot/P69708|https://www.uniprot.org/uniprot/P69707|https://www.uniprot.org/uniprot/P69706|https://www.uniprot.org/uniprot/P33515|https://www.uniprot.org/uniprot/P33478|https://www.uniprot.org/uniprot/P32886|https://www.uniprot.org/uniprot/P30026|https://www.uniprot.org/uniprot/P29991|https://www.uniprot.org/uniprot/P29990|https://www.uniprot.org/uniprot/P29983|https://www.uniprot.org/uniprot/P29838|https://www.uniprot.org/uniprot/P29837|https://www.uniprot.org/uniprot/P29178|https://www.uniprot.org/uniprot/P29165|https://www.uniprot.org/uniprot/P27915|https://www.uniprot.org/uniprot/P27913|https://www.uniprot.org/uniprot/P27912|https://www.uniprot.org/uniprot/P27910|https://www.uniprot.org/uniprot/P27909|https://www.uniprot.org/uniprot/P27395|https://www.uniprot.org/uniprot/P24023|https://www.uniprot.org/uniprot/P03151|https://www.uniprot.org/uniprot/P03150|https://www.uniprot.org/uniprot/P03149|https://www.uniprot.org/uniprot/P03148|https://www.uniprot.org/uniprot/P03147|https://www.uniprot.org/uniprot/P03146|https://www.uniprot.org/uniprot/O91857|https://www.uniprot.org/uniprot/O71303|https://www.uniprot.org/uniprot/O42028|https://www.uniprot.org/uniprot/O10383|https://www.uniprot.org/uniprot/H9A910|https://www.uniprot.org/uniprot/H8Y6L5|https://www.uniprot.org/uniprot/H8Y6L4|https://www.uniprot.org/uniprot/H8Y6L3|https://www.uniprot.org/uniprot/G3FEX6|https://www.uniprot.org/uniprot/D7RF80|https://www.uniprot.org/uniprot/C8XPB2|https://www.uniprot.org/uniprot/C8XPA8|https://www.uniprot.org/uniprot/C5H431|https://www.uniprot.org/uniprot/B1PMU9|https://www.uniprot.org/uniprot/A3EZ58|https://www.uniprot.org/uniprot/A0A165GB83|https://www.uniprot.org/uniprot/A0A142I5B9|https://www.uniprot.org/uniprot/A0A024B7W1|https://www.uniprot.org/uniprot/Q9YWN2|https://www.uniprot.org/uniprot/Q9YWN1|https://www.uniprot.org/uniprot/Q9YWN0|https://www.uniprot.org/uniprot/Q9YRV3|https://www.uniprot.org/uniprot/Q9WDA6|https://www.uniprot.org/uniprot/Q9W878|https://www.uniprot.org/uniprot/Q9QMI2|https://www.uniprot.org/uniprot/Q9QEW5|https://www.uniprot.org/uniprot/P22338|https://www.uniprot.org/uniprot/P19901|https://www.uniprot.org/uniprot/P19712|https://www.uniprot.org/uniprot/P19110|https://www.uniprot.org/uniprot/P17763|https://www.uniprot.org/uniprot/P17392|https://www.uniprot.org/uniprot/P17391|https://www.uniprot.org/uniprot/P14403|https://www.uniprot.org/uniprot/P14340|https://www.uniprot.org/uniprot/P14337|https://www.uniprot.org/uniprot/P14336|https://www.uniprot.org/uniprot/P14335|https://www.uniprot.org/uniprot/P12901|https://www.uniprot.org/uniprot/P12823|https://www.uniprot.org/uniprot/P0DOK8|https://www.uniprot.org/uniprot/P0DOH9|https://www.uniprot.org/uniprot/P0DOH8|https://www.uniprot.org/uniprot/P0DOH7|https://www.uniprot.org/uniprot/P0C6K3|https://www.uniprot.org/uniprot/P0C6K2|https://www.uniprot.org/uniprot/P0C6K1|https://www.uniprot.org/uniprot/P0C6K0|https://www.uniprot.org/uniprot/P0C6J8|https://www.uniprot.org/uniprot/P0C6J7|https://www.uniprot.org/uniprot/P0C6J1|https://www.uniprot.org/uniprot/P0C6I9|https://www.uniprot.org/uniprot/P0C6I8|https://www.uniprot.org/uniprot/P0C6I6|https://www.uniprot.org/uniprot/P0C6I4|https://www.uniprot.org/uniprot/P0C6I3|https://www.uniprot.org/uniprot/P0C6I2|https://www.uniprot.org/uniprot/P0C6H8|https://www.uniprot.org/uniprot/P0C6H7|https://www.uniprot.org/uniprot/P0C6H6|https://www.uniprot.org/uniprot/P0C6H4|https://www.uniprot.org/uniprot/P0C698|https://www.uniprot.org/uniprot/P0C697|https://www.uniprot.org/uniprot/P0C696|https://www.uniprot.org/uniprot/P0C695|https://www.uniprot.org/uniprot/P0C694|https://www.uniprot.org/uniprot/P0C693|https://www.uniprot.org/uniprot/P0C683|https://www.uniprot.org/uniprot/P0C682|https://www.uniprot.org/uniprot/P0C680|https://www.uniprot.org/uniprot/P0C677|https://www.uniprot.org/uniprot/P09866|https://www.uniprot.org/uniprot/P09732|https://www.uniprot.org/uniprot/P08769|https://www.uniprot.org/uniprot/P07721|https://www.uniprot.org/uniprot/P07720|https://www.uniprot.org/uniprot/P07565|https://www.uniprot.org/uniprot/P07564|https://www.uniprot.org/uniprot/P06935|https://www.uniprot.org/uniprot/P06433|https://www.uniprot.org/uniprot/P05769|https://www.uniprot.org/uniprot/P03314|https://www.uniprot.org/uniprot/P03152
T5717 4568-4571 Protein denotes CDR https://www.uniprot.org/uniprot/Q9NS54|https://www.uniprot.org/uniprot/Q95JH5|https://www.uniprot.org/uniprot/Q95JH4|https://www.uniprot.org/uniprot/Q8WW84|https://www.uniprot.org/uniprot/Q5T6A3|https://www.uniprot.org/uniprot/P17516

LitCovid-sample-PD-IDO

Id Subject Object Predicate Lexical cue
T161 1245-1249 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T162 1601-1605 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T163 2055-2059 http://purl.obolibrary.org/obo/BFO_0000029 denotes site
T164 4158-4168 http://purl.obolibrary.org/obo/IDO_0000607 denotes production

LitCovid-sample-PD-FMA

Id Subject Object Predicate Lexical cue fma_id
T212 101-109 Body_part denotes Proteins http://purl.org/sig/ont/fma/fma67257
T213 131-138 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T214 217-224 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T215 471-478 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T216 2183-2190 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T217 2240-2247 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T218 2253-2265 Body_part denotes glycoprotein http://purl.org/sig/ont/fma/fma62925
T219 2539-2546 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T220 3372-3384 Body_part denotes carbohydrate http://purl.org/sig/ont/fma/fma82737
T221 3389-3396 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T222 4100-4107 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T223 4523-4531 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871

LitCovid-sample-PD-GO-BP-0

Id Subject Object Predicate Lexical cue
T132 877-890 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T133 3497-3507 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation
T134 3603-3613 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation

LitCovid-sample-GO-BP

Id Subject Object Predicate Lexical cue
T125 877-890 http://purl.obolibrary.org/obo/GO_0070085 denotes glycosylation
T126 3497-3507 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation
T127 3603-3613 http://purl.obolibrary.org/obo/GO_0065007 denotes regulation

LitCovid-sample-Glycan

Id Subject Object Predicate Lexical cue
T2947 3009-3012 https://glytoucan.org/Structures/Glycans/G05518TD denotes All

2_test

Id Subject Object Predicate Lexical cue
32841605-32075877-19659565 340-344 32075877 denotes 2020
32841605-24375430-19659566 2488-2492 24375430 denotes 2014
32841605-28120784-19659567 2587-2591 28120784 denotes 2016
32841605-28017661-19659568 2606-2610 28017661 denotes 2017
32841605-22582031-19659569 3120-3124 22582031 denotes 2012
32841605-26592383-19659570 3149-3153 26592383 denotes 2013
32841605-17849372-19659571 3297-3301 17849372 denotes 2008
32841605-26574453-19659572 3344-3348 26574453 denotes 2015
32841605-8119250-19659573 3771-3775 8119250 denotes 1993